library(here)
library(tidyverse)
library(cowplot)
library(GGally)
theme_set(theme_light())
library(scuttle)
library(scater)
library(kableExtra)
library(DDCompanion)
Setup
## Directory setup
here_root <- "benchmarks/covid"
here::i_am(file.path(here_root, "analysis/covid-mock-results.Rmd"))
#> here() starts at /kyukon/data/gent/vo/000/gvo00063/Jeroen/DD_project_v2
res_dir <- here::here(here_root, "results")
fig_dir <- here::here(here_root, "figures")
- Using
methods: bGLM, qbGLM, qbGLM_offset, qbGLM_offset_squeeze, edgeR_NB, edgeR_QP, edgeR_NB_optim, edgeR_QP_optim
- Using
celltypes: class_switched_memory_B_cell_Healthy, immature_B_cell_Healthy, naive_B_cell_Healthy, class_switched_memory_B_cell_Mild, immature_B_cell_Mild, naive_B_cell_Mild, class_switched_memory_B_cell_Moderate, immature_B_cell_Moderate, naive_B_cell_Moderate, class_switched_memory_B_cell_Critical, immature_B_cell_Critical, naive_B_cell_Critical
- Using
datatype: pb
Load results
res_files <- map(celltypes, ~ get_mock_res_files(
dataset = "covid",
datatype = datatype,
methods = methods,
celltype = .x
)) %>%
set_names(celltypes)
#res_list <- map_depth(res_files, 2, readRDS)
res_list <- lapply(res_files, function(element){
lapply(element, readRDS)
})
## Check for expected data structure
stopifnot(unlist(map_depth(res_list, 3, ~ is.data.frame(.x$results))))
Load SCE objects
data_files <- map(celltypes, ~ get_SCE_files(
dataset = "covid", which = "mock_replicates",
celltype = .x
)) %>%
set_names(celltypes)
sce_objects <- map(data_files, readRDS)
Data overview
- The results were generated from 5 mock replicates
- Each replicate was generated by randomly splitting the subjects in two mock groups
- No sub-sampling of cells per patient was performed for this data
map_dfr(sce_objects,
~ map_dfr(.x, function(x) c(nrows = nrow(x), ncols = ncol(x)),
.id = "replicate"
),
.id = "celltypes"
)
Subjects are divided across mock groups as follows:
map(sce_objects[[1]], function(x) table(x$donor_id, x$mock_group))
#> $replicate_1
#>
#> A B
#> CV0902 49 0
#> CV0904 102 0
#> CV0911 0 23
#> CV0915 26 0
#> CV0917 21 0
#> CV0926 0 23
#> CV0929 0 48
#> CV0934 0 55
#> MH8919178 99 0
#> MH8919227 0 44
#> MH8919282 0 51
#> MH8919283 80 0
#> MH8919333 0 229
#> newcastle74 89 0
#>
#> $replicate_2
#>
#> A B
#> CV0902 49 0
#> CV0904 102 0
#> CV0911 23 0
#> CV0915 0 26
#> CV0917 0 21
#> CV0926 0 23
#> CV0929 0 48
#> CV0934 55 0
#> MH8919178 0 99
#> MH8919227 44 0
#> MH8919282 51 0
#> MH8919283 0 80
#> MH8919333 229 0
#> newcastle74 0 89
#>
#> $replicate_3
#>
#> A B
#> CV0902 49 0
#> CV0904 102 0
#> CV0911 0 23
#> CV0915 26 0
#> CV0917 21 0
#> CV0926 0 23
#> CV0929 0 48
#> CV0934 0 55
#> MH8919178 99 0
#> MH8919227 44 0
#> MH8919282 51 0
#> MH8919283 0 80
#> MH8919333 0 229
#> newcastle74 0 89
#>
#> $replicate_4
#>
#> A B
#> CV0902 0 49
#> CV0904 102 0
#> CV0911 23 0
#> CV0915 0 26
#> CV0917 21 0
#> CV0926 0 23
#> CV0929 48 0
#> CV0934 0 55
#> MH8919178 0 99
#> MH8919227 0 44
#> MH8919282 0 51
#> MH8919283 80 0
#> MH8919333 229 0
#> newcastle74 89 0
#>
#> $replicate_5
#>
#> A B
#> CV0902 49 0
#> CV0904 0 102
#> CV0911 23 0
#> CV0915 0 26
#> CV0917 0 21
#> CV0926 23 0
#> CV0929 0 48
#> CV0934 55 0
#> MH8919178 0 99
#> MH8919227 44 0
#> MH8919282 51 0
#> MH8919283 0 80
#> MH8919333 0 229
#> newcastle74 89 0
Visualize results
Run times
runtime_plots <- imap(runtimes,
~ plot_run_times(.x, width = 0.2, height = 0) +
ggtitle(.y)
)
class_switched_memory_B_cell_Healthy

immature_B_cell_Healthy

naive_B_cell_Healthy

class_switched_memory_B_cell_Mild

immature_B_cell_Mild

naive_B_cell_Mild

class_switched_memory_B_cell_Moderate

immature_B_cell_Moderate

naive_B_cell_Moderate

class_switched_memory_B_cell_Critical

immature_B_cell_Critical

naive_B_cell_Critical

Number of significant genes for different FDR levels
n_sign_summaries <- map(res_tables, function(tmp) {
tmp %>%
group_by(replicate, method) %>%
summarise(
sum(FDR < 0.01),
sum(FDR < 0.05),
sum(FDR < 0.1),
.groups = "drop"
)
})
class_switched_memory_B_cell_Healthy
Cells per patient: class_switched_memory_B_cell_Healthy
|
method
|
sum(FDR < 0.01)
|
sum(FDR < 0.05)
|
sum(FDR < 0.1)
|
|
Replicate: 1
|
|
bGLM
|
10
|
17
|
22
|
|
edgeR_NB
|
0
|
0
|
1
|
|
edgeR_NB_optim
|
2
|
4
|
6
|
|
edgeR_QP
|
0
|
0
|
0
|
|
edgeR_QP_optim
|
3
|
5
|
5
|
|
qbGLM
|
295
|
302
|
309
|
|
qbGLM_offset
|
292
|
298
|
314
|
|
qbGLM_offset_squeeze
|
1
|
2
|
2
|
|
Replicate: 2
|
|
bGLM
|
15
|
34
|
43
|
|
edgeR_NB
|
0
|
0
|
0
|
|
edgeR_NB_optim
|
0
|
1
|
2
|
|
edgeR_QP
|
0
|
0
|
0
|
|
edgeR_QP_optim
|
0
|
2
|
2
|
|
qbGLM
|
298
|
303
|
310
|
|
qbGLM_offset
|
293
|
301
|
318
|
|
qbGLM_offset_squeeze
|
1
|
3
|
3
|
|
Replicate: 3
|
|
bGLM
|
608
|
1375
|
1933
|
|
edgeR_NB
|
0
|
10
|
62
|
|
edgeR_NB_optim
|
0
|
5
|
7
|
|
edgeR_QP
|
0
|
80
|
297
|
|
edgeR_QP_optim
|
0
|
3
|
7
|
|
qbGLM
|
312
|
416
|
623
|
|
qbGLM_offset
|
300
|
322
|
347
|
|
qbGLM_offset_squeeze
|
0
|
1
|
1
|
|
Replicate: 4
|
|
bGLM
|
513
|
1231
|
1883
|
|
edgeR_NB
|
3
|
9
|
37
|
|
edgeR_NB_optim
|
0
|
4
|
17
|
|
edgeR_QP
|
4
|
38
|
155
|
|
edgeR_QP_optim
|
0
|
4
|
18
|
|
qbGLM
|
315
|
404
|
554
|
|
qbGLM_offset
|
302
|
319
|
342
|
|
qbGLM_offset_squeeze
|
0
|
2
|
3
|
|
Replicate: 5
|
|
bGLM
|
23
|
86
|
192
|
|
edgeR_NB
|
0
|
0
|
2
|
|
edgeR_NB_optim
|
1
|
2
|
3
|
|
edgeR_QP
|
1
|
2
|
2
|
|
edgeR_QP_optim
|
1
|
2
|
2
|
|
qbGLM
|
295
|
314
|
326
|
|
qbGLM_offset
|
294
|
308
|
323
|
|
qbGLM_offset_squeeze
|
0
|
1
|
1
|
immature_B_cell_Healthy
Cells per patient: immature_B_cell_Healthy
|
method
|
sum(FDR < 0.01)
|
sum(FDR < 0.05)
|
sum(FDR < 0.1)
|
|
Replicate: 1
|
|
bGLM
|
20
|
82
|
203
|
|
edgeR_NB
|
0
|
0
|
0
|
|
edgeR_NB_optim
|
0
|
0
|
0
|
|
edgeR_QP
|
1
|
1
|
1
|
|
edgeR_QP_optim
|
0
|
0
|
0
|
|
qbGLM
|
50
|
50
|
54
|
|
qbGLM_offset
|
50
|
53
|
54
|
|
qbGLM_offset_squeeze
|
0
|
1
|
1
|
|
Replicate: 2
|
|
bGLM
|
0
|
3
|
4
|
|
edgeR_NB
|
0
|
0
|
0
|
|
edgeR_NB_optim
|
0
|
0
|
0
|
|
edgeR_QP
|
0
|
0
|
0
|
|
edgeR_QP_optim
|
0
|
0
|
0
|
|
qbGLM
|
56
|
59
|
59
|
|
qbGLM_offset
|
54
|
54
|
57
|
|
qbGLM_offset_squeeze
|
0
|
0
|
0
|
|
Replicate: 3
|
|
bGLM
|
3
|
5
|
5
|
|
edgeR_NB
|
0
|
0
|
0
|
|
edgeR_NB_optim
|
0
|
0
|
0
|
|
edgeR_QP
|
0
|
0
|
0
|
|
edgeR_QP_optim
|
0
|
0
|
0
|
|
qbGLM
|
54
|
57
|
57
|
|
qbGLM_offset
|
54
|
54
|
55
|
|
qbGLM_offset_squeeze
|
0
|
0
|
0
|
|
Replicate: 4
|
|
bGLM
|
243
|
629
|
1038
|
|
edgeR_NB
|
0
|
1
|
13
|
|
edgeR_NB_optim
|
3
|
3
|
3
|
|
edgeR_QP
|
1
|
21
|
33
|
|
edgeR_QP_optim
|
3
|
3
|
3
|
|
qbGLM
|
49
|
56
|
68
|
|
qbGLM_offset
|
50
|
54
|
57
|
|
qbGLM_offset_squeeze
|
0
|
0
|
0
|
|
Replicate: 5
|
|
bGLM
|
7
|
14
|
52
|
|
edgeR_NB
|
0
|
0
|
0
|
|
edgeR_NB_optim
|
0
|
0
|
0
|
|
edgeR_QP
|
1
|
1
|
1
|
|
edgeR_QP_optim
|
0
|
0
|
0
|
|
qbGLM
|
49
|
50
|
54
|
|
qbGLM_offset
|
50
|
53
|
53
|
|
qbGLM_offset_squeeze
|
0
|
1
|
1
|
naive_B_cell_Healthy
Cells per patient: naive_B_cell_Healthy
|
method
|
sum(FDR < 0.01)
|
sum(FDR < 0.05)
|
sum(FDR < 0.1)
|
|
Replicate: 1
|
|
bGLM
|
4984
|
6439
|
7249
|
|
edgeR_NB
|
0
|
1
|
2
|
|
edgeR_NB_optim
|
25
|
52
|
77
|
|
edgeR_QP
|
125
|
1896
|
3995
|
|
edgeR_QP_optim
|
119
|
233
|
333
|
|
qbGLM
|
1
|
11
|
2596
|
|
qbGLM_offset
|
1
|
3
|
4
|
|
qbGLM_offset_squeeze
|
1
|
3
|
24
|
|
Replicate: 2
|
|
bGLM
|
1972
|
3188
|
3953
|
|
edgeR_NB
|
0
|
0
|
0
|
|
edgeR_NB_optim
|
13
|
23
|
25
|
|
edgeR_QP
|
0
|
2
|
2
|
|
edgeR_QP_optim
|
30
|
52
|
63
|
|
qbGLM
|
0
|
0
|
0
|
|
qbGLM_offset
|
0
|
0
|
0
|
|
qbGLM_offset_squeeze
|
0
|
0
|
0
|
|
Replicate: 3
|
|
bGLM
|
2217
|
3668
|
4635
|
|
edgeR_NB
|
0
|
0
|
0
|
|
edgeR_NB_optim
|
7
|
13
|
18
|
|
edgeR_QP
|
0
|
1
|
1
|
|
edgeR_QP_optim
|
15
|
25
|
44
|
|
qbGLM
|
0
|
0
|
0
|
|
qbGLM_offset
|
0
|
0
|
0
|
|
qbGLM_offset_squeeze
|
0
|
0
|
0
|
|
Replicate: 4
|
|
bGLM
|
96
|
188
|
268
|
|
edgeR_NB
|
0
|
0
|
0
|
|
edgeR_NB_optim
|
12
|
15
|
24
|
|
edgeR_QP
|
0
|
1
|
2
|
|
edgeR_QP_optim
|
16
|
29
|
34
|
|
qbGLM
|
0
|
1
|
1
|
|
qbGLM_offset
|
1
|
1
|
2
|
|
qbGLM_offset_squeeze
|
0
|
0
|
0
|
|
Replicate: 5
|
|
bGLM
|
1082
|
2044
|
2779
|
|
edgeR_NB
|
1
|
1
|
1
|
|
edgeR_NB_optim
|
18
|
32
|
46
|
|
edgeR_QP
|
1
|
1
|
1
|
|
edgeR_QP_optim
|
29
|
62
|
71
|
|
qbGLM
|
0
|
0
|
0
|
|
qbGLM_offset
|
0
|
0
|
0
|
|
qbGLM_offset_squeeze
|
0
|
0
|
0
|
class_switched_memory_B_cell_Mild
Cells per patient: class_switched_memory_B_cell_Mild
|
method
|
sum(FDR < 0.01)
|
sum(FDR < 0.05)
|
sum(FDR < 0.1)
|
|
Replicate: 1
|
|
bGLM
|
9
|
25
|
47
|
|
edgeR_NB
|
1
|
1
|
1
|
|
edgeR_NB_optim
|
1
|
1
|
1
|
|
edgeR_QP
|
1
|
1
|
1
|
|
edgeR_QP_optim
|
1
|
1
|
1
|
|
qbGLM
|
0
|
1
|
1
|
|
qbGLM_offset
|
0
|
1
|
1
|
|
qbGLM_offset_squeeze
|
0
|
0
|
0
|
|
Replicate: 2
|
|
bGLM
|
14
|
33
|
48
|
|
edgeR_NB
|
5
|
6
|
6
|
|
edgeR_NB_optim
|
6
|
8
|
10
|
|
edgeR_QP
|
5
|
12
|
13
|
|
edgeR_QP_optim
|
6
|
11
|
13
|
|
qbGLM
|
0
|
2
|
2
|
|
qbGLM_offset
|
2
|
2
|
2
|
|
qbGLM_offset_squeeze
|
0
|
0
|
1
|
|
Replicate: 3
|
|
bGLM
|
97
|
307
|
465
|
|
edgeR_NB
|
3
|
13
|
38
|
|
edgeR_NB_optim
|
2
|
3
|
3
|
|
edgeR_QP
|
3
|
14
|
56
|
|
edgeR_QP_optim
|
2
|
3
|
3
|
|
qbGLM
|
1
|
1
|
7
|
|
qbGLM_offset
|
1
|
2
|
2
|
|
qbGLM_offset_squeeze
|
0
|
1
|
1
|
|
Replicate: 4
|
|
bGLM
|
5
|
5
|
9
|
|
edgeR_NB
|
1
|
1
|
1
|
|
edgeR_NB_optim
|
0
|
1
|
3
|
|
edgeR_QP
|
1
|
2
|
2
|
|
edgeR_QP_optim
|
0
|
3
|
3
|
|
qbGLM
|
0
|
1
|
1
|
|
qbGLM_offset
|
0
|
1
|
1
|
|
qbGLM_offset_squeeze
|
0
|
0
|
0
|
|
Replicate: 5
|
|
bGLM
|
22
|
42
|
46
|
|
edgeR_NB
|
7
|
9
|
12
|
|
edgeR_NB_optim
|
12
|
14
|
15
|
|
edgeR_QP
|
7
|
11
|
15
|
|
edgeR_QP_optim
|
11
|
14
|
16
|
|
qbGLM
|
0
|
0
|
1
|
|
qbGLM_offset
|
0
|
0
|
1
|
|
qbGLM_offset_squeeze
|
0
|
0
|
0
|
immature_B_cell_Mild
Cells per patient: immature_B_cell_Mild
|
method
|
sum(FDR < 0.01)
|
sum(FDR < 0.05)
|
sum(FDR < 0.1)
|
|
Replicate: 1
|
|
bGLM
|
7
|
15
|
18
|
|
edgeR_NB
|
1
|
2
|
3
|
|
edgeR_NB_optim
|
1
|
1
|
1
|
|
edgeR_QP
|
1
|
1
|
2
|
|
edgeR_QP_optim
|
1
|
1
|
2
|
|
qbGLM
|
0
|
0
|
0
|
|
qbGLM_offset
|
0
|
0
|
0
|
|
qbGLM_offset_squeeze
|
0
|
0
|
0
|
|
Replicate: 2
|
|
bGLM
|
2
|
5
|
6
|
|
edgeR_NB
|
0
|
0
|
0
|
|
edgeR_NB_optim
|
0
|
0
|
0
|
|
edgeR_QP
|
0
|
0
|
0
|
|
edgeR_QP_optim
|
0
|
0
|
1
|
|
qbGLM
|
0
|
0
|
0
|
|
qbGLM_offset
|
0
|
0
|
1
|
|
qbGLM_offset_squeeze
|
0
|
0
|
0
|
|
Replicate: 3
|
|
bGLM
|
1
|
8
|
13
|
|
edgeR_NB
|
1
|
1
|
1
|
|
edgeR_NB_optim
|
1
|
2
|
2
|
|
edgeR_QP
|
1
|
1
|
1
|
|
edgeR_QP_optim
|
0
|
2
|
2
|
|
qbGLM
|
0
|
0
|
0
|
|
qbGLM_offset
|
0
|
0
|
0
|
|
qbGLM_offset_squeeze
|
0
|
0
|
0
|
|
Replicate: 4
|
|
bGLM
|
13
|
24
|
34
|
|
edgeR_NB
|
0
|
0
|
1
|
|
edgeR_NB_optim
|
0
|
1
|
2
|
|
edgeR_QP
|
0
|
0
|
1
|
|
edgeR_QP_optim
|
0
|
1
|
2
|
|
qbGLM
|
0
|
0
|
0
|
|
qbGLM_offset
|
0
|
0
|
0
|
|
qbGLM_offset_squeeze
|
0
|
0
|
0
|
|
Replicate: 5
|
|
bGLM
|
7
|
9
|
11
|
|
edgeR_NB
|
0
|
0
|
0
|
|
edgeR_NB_optim
|
0
|
1
|
1
|
|
edgeR_QP
|
0
|
0
|
0
|
|
edgeR_QP_optim
|
0
|
1
|
1
|
|
qbGLM
|
0
|
0
|
0
|
|
qbGLM_offset
|
0
|
0
|
0
|
|
qbGLM_offset_squeeze
|
0
|
0
|
0
|
naive_B_cell_Mild
Cells per patient: naive_B_cell_Mild
|
method
|
sum(FDR < 0.01)
|
sum(FDR < 0.05)
|
sum(FDR < 0.1)
|
|
Replicate: 1
|
|
bGLM
|
744
|
1210
|
1594
|
|
edgeR_NB
|
0
|
0
|
1
|
|
edgeR_NB_optim
|
0
|
1
|
1
|
|
edgeR_QP
|
1
|
1
|
2
|
|
edgeR_QP_optim
|
1
|
1
|
3
|
|
qbGLM
|
84
|
92
|
96
|
|
qbGLM_offset
|
85
|
93
|
106
|
|
qbGLM_offset_squeeze
|
0
|
0
|
0
|
|
Replicate: 2
|
|
bGLM
|
338
|
608
|
845
|
|
edgeR_NB
|
0
|
0
|
0
|
|
edgeR_NB_optim
|
0
|
0
|
0
|
|
edgeR_QP
|
0
|
0
|
0
|
|
edgeR_QP_optim
|
0
|
0
|
0
|
|
qbGLM
|
86
|
88
|
92
|
|
qbGLM_offset
|
86
|
88
|
92
|
|
qbGLM_offset_squeeze
|
0
|
0
|
0
|
|
Replicate: 3
|
|
bGLM
|
867
|
1425
|
1853
|
|
edgeR_NB
|
0
|
0
|
0
|
|
edgeR_NB_optim
|
1
|
2
|
2
|
|
edgeR_QP
|
0
|
0
|
0
|
|
edgeR_QP_optim
|
1
|
2
|
4
|
|
qbGLM
|
85
|
94
|
103
|
|
qbGLM_offset
|
89
|
97
|
105
|
|
qbGLM_offset_squeeze
|
1
|
3
|
6
|
|
Replicate: 4
|
|
bGLM
|
378
|
690
|
909
|
|
edgeR_NB
|
0
|
0
|
0
|
|
edgeR_NB_optim
|
0
|
0
|
0
|
|
edgeR_QP
|
3
|
6
|
7
|
|
edgeR_QP_optim
|
3
|
7
|
8
|
|
qbGLM
|
82
|
84
|
89
|
|
qbGLM_offset
|
82
|
90
|
94
|
|
qbGLM_offset_squeeze
|
0
|
0
|
0
|
|
Replicate: 5
|
|
bGLM
|
384
|
800
|
1163
|
|
edgeR_NB
|
0
|
0
|
0
|
|
edgeR_NB_optim
|
0
|
0
|
0
|
|
edgeR_QP
|
0
|
0
|
0
|
|
edgeR_QP_optim
|
0
|
0
|
3
|
|
qbGLM
|
84
|
85
|
86
|
|
qbGLM_offset
|
84
|
86
|
92
|
|
qbGLM_offset_squeeze
|
0
|
0
|
0
|
class_switched_memory_B_cell_Moderate
Cells per patient: class_switched_memory_B_cell_Moderate
|
method
|
sum(FDR < 0.01)
|
sum(FDR < 0.05)
|
sum(FDR < 0.1)
|
|
Replicate: 1
|
|
bGLM
|
13
|
37
|
56
|
|
edgeR_NB
|
0
|
0
|
0
|
|
edgeR_NB_optim
|
0
|
0
|
0
|
|
edgeR_QP
|
0
|
0
|
0
|
|
edgeR_QP_optim
|
0
|
0
|
0
|
|
qbGLM
|
0
|
0
|
0
|
|
qbGLM_offset
|
0
|
0
|
0
|
|
qbGLM_offset_squeeze
|
0
|
0
|
0
|
|
Replicate: 2
|
|
bGLM
|
25
|
63
|
101
|
|
edgeR_NB
|
0
|
2
|
3
|
|
edgeR_NB_optim
|
2
|
2
|
3
|
|
edgeR_QP
|
1
|
3
|
3
|
|
edgeR_QP_optim
|
2
|
4
|
14
|
|
qbGLM
|
0
|
0
|
0
|
|
qbGLM_offset
|
0
|
0
|
0
|
|
qbGLM_offset_squeeze
|
0
|
0
|
0
|
|
Replicate: 3
|
|
bGLM
|
41
|
83
|
136
|
|
edgeR_NB
|
0
|
0
|
0
|
|
edgeR_NB_optim
|
1
|
1
|
3
|
|
edgeR_QP
|
0
|
0
|
4
|
|
edgeR_QP_optim
|
1
|
2
|
3
|
|
qbGLM
|
1
|
1
|
1
|
|
qbGLM_offset
|
0
|
0
|
0
|
|
qbGLM_offset_squeeze
|
0
|
0
|
0
|
|
Replicate: 4
|
|
bGLM
|
33
|
67
|
93
|
|
edgeR_NB
|
0
|
0
|
0
|
|
edgeR_NB_optim
|
0
|
1
|
5
|
|
edgeR_QP
|
0
|
0
|
0
|
|
edgeR_QP_optim
|
0
|
5
|
13
|
|
qbGLM
|
1
|
1
|
1
|
|
qbGLM_offset
|
0
|
0
|
0
|
|
qbGLM_offset_squeeze
|
0
|
0
|
0
|
|
Replicate: 5
|
|
bGLM
|
15
|
21
|
31
|
|
edgeR_NB
|
0
|
0
|
1
|
|
edgeR_NB_optim
|
1
|
1
|
1
|
|
edgeR_QP
|
0
|
0
|
0
|
|
edgeR_QP_optim
|
1
|
2
|
3
|
|
qbGLM
|
1
|
1
|
1
|
|
qbGLM_offset
|
0
|
0
|
0
|
|
qbGLM_offset_squeeze
|
0
|
0
|
0
|
immature_B_cell_Moderate
Cells per patient: immature_B_cell_Moderate
|
method
|
sum(FDR < 0.01)
|
sum(FDR < 0.05)
|
sum(FDR < 0.1)
|
|
Replicate: 1
|
|
bGLM
|
29
|
46
|
65
|
|
edgeR_NB
|
0
|
1
|
2
|
|
edgeR_NB_optim
|
3
|
6
|
6
|
|
edgeR_QP
|
2
|
2
|
3
|
|
edgeR_QP_optim
|
5
|
7
|
9
|
|
qbGLM
|
3
|
3
|
3
|
|
qbGLM_offset
|
0
|
0
|
0
|
|
qbGLM_offset_squeeze
|
0
|
0
|
0
|
|
Replicate: 2
|
|
bGLM
|
6
|
18
|
30
|
|
edgeR_NB
|
0
|
0
|
0
|
|
edgeR_NB_optim
|
0
|
0
|
0
|
|
edgeR_QP
|
0
|
0
|
2
|
|
edgeR_QP_optim
|
0
|
2
|
2
|
|
qbGLM
|
4
|
4
|
4
|
|
qbGLM_offset
|
1
|
1
|
1
|
|
qbGLM_offset_squeeze
|
0
|
0
|
0
|
|
Replicate: 3
|
|
bGLM
|
2
|
9
|
13
|
|
edgeR_NB
|
0
|
0
|
0
|
|
edgeR_NB_optim
|
0
|
0
|
0
|
|
edgeR_QP
|
0
|
0
|
0
|
|
edgeR_QP_optim
|
0
|
0
|
0
|
|
qbGLM
|
4
|
4
|
4
|
|
qbGLM_offset
|
1
|
1
|
1
|
|
qbGLM_offset_squeeze
|
0
|
0
|
0
|
|
Replicate: 4
|
|
bGLM
|
33
|
66
|
98
|
|
edgeR_NB
|
0
|
1
|
1
|
|
edgeR_NB_optim
|
0
|
12
|
25
|
|
edgeR_QP
|
0
|
3
|
13
|
|
edgeR_QP_optim
|
0
|
16
|
29
|
|
qbGLM
|
1
|
1
|
1
|
|
qbGLM_offset
|
1
|
1
|
1
|
|
qbGLM_offset_squeeze
|
0
|
0
|
0
|
|
Replicate: 5
|
|
bGLM
|
25
|
43
|
57
|
|
edgeR_NB
|
0
|
1
|
1
|
|
edgeR_NB_optim
|
3
|
3
|
3
|
|
edgeR_QP
|
3
|
3
|
4
|
|
edgeR_QP_optim
|
3
|
3
|
3
|
|
qbGLM
|
1
|
1
|
1
|
|
qbGLM_offset
|
1
|
1
|
2
|
|
qbGLM_offset_squeeze
|
0
|
0
|
0
|
naive_B_cell_Moderate
Cells per patient: naive_B_cell_Moderate
|
method
|
sum(FDR < 0.01)
|
sum(FDR < 0.05)
|
sum(FDR < 0.1)
|
|
Replicate: 1
|
|
bGLM
|
1470
|
2221
|
2758
|
|
edgeR_NB
|
0
|
0
|
0
|
|
edgeR_NB_optim
|
0
|
0
|
0
|
|
edgeR_QP
|
0
|
0
|
0
|
|
edgeR_QP_optim
|
0
|
0
|
0
|
|
qbGLM
|
62
|
64
|
70
|
|
qbGLM_offset
|
62
|
66
|
75
|
|
qbGLM_offset_squeeze
|
0
|
0
|
0
|
|
Replicate: 2
|
|
bGLM
|
2336
|
3403
|
4150
|
|
edgeR_NB
|
0
|
0
|
0
|
|
edgeR_NB_optim
|
0
|
0
|
0
|
|
edgeR_QP
|
0
|
0
|
29
|
|
edgeR_QP_optim
|
1
|
40
|
248
|
|
qbGLM
|
62
|
66
|
75
|
|
qbGLM_offset
|
64
|
86
|
161
|
|
qbGLM_offset_squeeze
|
0
|
1
|
1
|
|
Replicate: 3
|
|
bGLM
|
2233
|
3228
|
3935
|
|
edgeR_NB
|
0
|
0
|
0
|
|
edgeR_NB_optim
|
0
|
0
|
1
|
|
edgeR_QP
|
0
|
2
|
6
|
|
edgeR_QP_optim
|
0
|
12
|
68
|
|
qbGLM
|
62
|
65
|
70
|
|
qbGLM_offset
|
65
|
79
|
117
|
|
qbGLM_offset_squeeze
|
0
|
0
|
0
|
|
Replicate: 4
|
|
bGLM
|
1056
|
1809
|
2390
|
|
edgeR_NB
|
0
|
0
|
0
|
|
edgeR_NB_optim
|
0
|
0
|
0
|
|
edgeR_QP
|
0
|
0
|
0
|
|
edgeR_QP_optim
|
0
|
0
|
0
|
|
qbGLM
|
62
|
63
|
63
|
|
qbGLM_offset
|
62
|
63
|
67
|
|
qbGLM_offset_squeeze
|
0
|
0
|
0
|
|
Replicate: 5
|
|
bGLM
|
1100
|
1736
|
2220
|
|
edgeR_NB
|
0
|
0
|
0
|
|
edgeR_NB_optim
|
0
|
1
|
1
|
|
edgeR_QP
|
1
|
1
|
1
|
|
edgeR_QP_optim
|
1
|
1
|
1
|
|
qbGLM
|
63
|
64
|
69
|
|
qbGLM_offset
|
63
|
72
|
78
|
|
qbGLM_offset_squeeze
|
0
|
0
|
0
|
class_switched_memory_B_cell_Critical
Cells per patient: class_switched_memory_B_cell_Critical
|
method
|
sum(FDR < 0.01)
|
sum(FDR < 0.05)
|
sum(FDR < 0.1)
|
|
Replicate: 1
|
|
bGLM
|
0
|
0
|
2
|
|
edgeR_NB
|
0
|
0
|
0
|
|
edgeR_NB_optim
|
0
|
0
|
0
|
|
edgeR_QP
|
0
|
0
|
0
|
|
edgeR_QP_optim
|
0
|
0
|
0
|
|
qbGLM
|
608
|
633
|
646
|
|
qbGLM_offset
|
623
|
639
|
670
|
|
qbGLM_offset_squeeze
|
0
|
1
|
8
|
|
Replicate: 2
|
|
bGLM
|
1
|
5
|
8
|
|
edgeR_NB
|
0
|
1
|
1
|
|
edgeR_NB_optim
|
1
|
1
|
1
|
|
edgeR_QP
|
1
|
1
|
1
|
|
edgeR_QP_optim
|
1
|
1
|
1
|
|
qbGLM
|
610
|
628
|
649
|
|
qbGLM_offset
|
619
|
633
|
662
|
|
qbGLM_offset_squeeze
|
0
|
1
|
1
|
|
Replicate: 3
|
|
bGLM
|
3
|
4
|
15
|
|
edgeR_NB
|
0
|
1
|
1
|
|
edgeR_NB_optim
|
1
|
1
|
3
|
|
edgeR_QP
|
1
|
1
|
1
|
|
edgeR_QP_optim
|
1
|
1
|
6
|
|
qbGLM
|
625
|
653
|
689
|
|
qbGLM_offset
|
625
|
656
|
687
|
|
qbGLM_offset_squeeze
|
0
|
1
|
9
|
|
Replicate: 4
|
|
bGLM
|
26
|
58
|
79
|
|
edgeR_NB
|
1
|
1
|
2
|
|
edgeR_NB_optim
|
5
|
13
|
17
|
|
edgeR_QP
|
6
|
7
|
9
|
|
edgeR_QP_optim
|
6
|
12
|
17
|
|
qbGLM
|
618
|
647
|
679
|
|
qbGLM_offset
|
630
|
665
|
711
|
|
qbGLM_offset_squeeze
|
0
|
2
|
12
|
|
Replicate: 5
|
|
bGLM
|
121
|
412
|
634
|
|
edgeR_NB
|
10
|
17
|
32
|
|
edgeR_NB_optim
|
6
|
14
|
23
|
|
edgeR_QP
|
13
|
33
|
62
|
|
edgeR_QP_optim
|
6
|
21
|
25
|
|
qbGLM
|
629
|
695
|
802
|
|
qbGLM_offset
|
620
|
653
|
682
|
|
qbGLM_offset_squeeze
|
0
|
1
|
11
|
immature_B_cell_Critical
Cells per patient: immature_B_cell_Critical
|
method
|
sum(FDR < 0.01)
|
sum(FDR < 0.05)
|
sum(FDR < 0.1)
|
|
Replicate: 1
|
|
bGLM
|
0
|
5
|
6
|
|
edgeR_NB
|
0
|
0
|
0
|
|
edgeR_NB_optim
|
0
|
0
|
0
|
|
edgeR_QP
|
0
|
0
|
0
|
|
edgeR_QP_optim
|
0
|
0
|
0
|
|
qbGLM
|
769
|
780
|
792
|
|
qbGLM_offset
|
765
|
785
|
804
|
|
qbGLM_offset_squeeze
|
0
|
11
|
11
|
|
Replicate: 2
|
|
bGLM
|
0
|
2
|
3
|
|
edgeR_NB
|
0
|
0
|
0
|
|
edgeR_NB_optim
|
0
|
0
|
0
|
|
edgeR_QP
|
0
|
0
|
0
|
|
edgeR_QP_optim
|
0
|
0
|
0
|
|
qbGLM
|
764
|
782
|
792
|
|
qbGLM_offset
|
764
|
781
|
798
|
|
qbGLM_offset_squeeze
|
0
|
10
|
10
|
|
Replicate: 3
|
|
bGLM
|
0
|
0
|
1
|
|
edgeR_NB
|
0
|
0
|
0
|
|
edgeR_NB_optim
|
0
|
0
|
0
|
|
edgeR_QP
|
0
|
0
|
0
|
|
edgeR_QP_optim
|
0
|
0
|
0
|
|
qbGLM
|
770
|
782
|
794
|
|
qbGLM_offset
|
771
|
789
|
813
|
|
qbGLM_offset_squeeze
|
0
|
11
|
56
|
|
Replicate: 4
|
|
bGLM
|
18
|
47
|
63
|
|
edgeR_NB
|
1
|
1
|
2
|
|
edgeR_NB_optim
|
6
|
9
|
12
|
|
edgeR_QP
|
5
|
7
|
8
|
|
edgeR_QP_optim
|
7
|
9
|
12
|
|
qbGLM
|
771
|
791
|
811
|
|
qbGLM_offset
|
772
|
791
|
826
|
|
qbGLM_offset_squeeze
|
9
|
11
|
54
|
|
Replicate: 5
|
|
bGLM
|
23
|
83
|
148
|
|
edgeR_NB
|
1
|
1
|
1
|
|
edgeR_NB_optim
|
0
|
1
|
1
|
|
edgeR_QP
|
3
|
3
|
3
|
|
edgeR_QP_optim
|
0
|
1
|
5
|
|
qbGLM
|
776
|
810
|
872
|
|
qbGLM_offset
|
774
|
794
|
848
|
|
qbGLM_offset_squeeze
|
9
|
9
|
56
|
naive_B_cell_Critical
Cells per patient: naive_B_cell_Critical
|
method
|
sum(FDR < 0.01)
|
sum(FDR < 0.05)
|
sum(FDR < 0.1)
|
|
Replicate: 1
|
|
bGLM
|
1005
|
1624
|
2113
|
|
edgeR_NB
|
0
|
0
|
0
|
|
edgeR_NB_optim
|
26
|
50
|
58
|
|
edgeR_QP
|
22
|
45
|
85
|
|
edgeR_QP_optim
|
130
|
193
|
251
|
|
qbGLM
|
466
|
488
|
516
|
|
qbGLM_offset
|
475
|
521
|
587
|
|
qbGLM_offset_squeeze
|
0
|
7
|
7
|
|
Replicate: 2
|
|
bGLM
|
2314
|
3438
|
4248
|
|
edgeR_NB
|
1
|
2
|
4
|
|
edgeR_NB_optim
|
27
|
51
|
65
|
|
edgeR_QP
|
66
|
153
|
352
|
|
edgeR_QP_optim
|
122
|
187
|
257
|
|
qbGLM
|
314
|
388
|
490
|
|
qbGLM_offset
|
309
|
359
|
413
|
|
qbGLM_offset_squeeze
|
0
|
0
|
0
|
|
Replicate: 3
|
|
bGLM
|
840
|
1363
|
1828
|
|
edgeR_NB
|
2
|
2
|
2
|
|
edgeR_NB_optim
|
30
|
40
|
46
|
|
edgeR_QP
|
37
|
56
|
71
|
|
edgeR_QP_optim
|
119
|
195
|
241
|
|
qbGLM
|
292
|
302
|
330
|
|
qbGLM_offset
|
295
|
325
|
371
|
|
qbGLM_offset_squeeze
|
0
|
4
|
9
|
|
Replicate: 4
|
|
bGLM
|
803
|
1721
|
2559
|
|
edgeR_NB
|
5
|
11
|
14
|
|
edgeR_NB_optim
|
19
|
34
|
42
|
|
edgeR_QP
|
20
|
42
|
54
|
|
edgeR_QP_optim
|
42
|
70
|
88
|
|
qbGLM
|
409
|
444
|
473
|
|
qbGLM_offset
|
410
|
439
|
483
|
|
qbGLM_offset_squeeze
|
0
|
4
|
5
|
|
Replicate: 5
|
|
bGLM
|
1607
|
2598
|
3280
|
|
edgeR_NB
|
1
|
1
|
1
|
|
edgeR_NB_optim
|
23
|
36
|
56
|
|
edgeR_QP
|
79
|
164
|
293
|
|
edgeR_QP_optim
|
115
|
194
|
241
|
|
qbGLM
|
285
|
305
|
345
|
|
qbGLM_offset
|
289
|
311
|
351
|
|
qbGLM_offset_squeeze
|
0
|
0
|
0
|
P-value distributions
pval_figs <- map(res_tables, pval_hist)
class_switched_memory_B_cell_Healthy

immature_B_cell_Healthy

naive_B_cell_Healthy

class_switched_memory_B_cell_Mild

immature_B_cell_Mild

naive_B_cell_Mild

class_switched_memory_B_cell_Moderate

immature_B_cell_Moderate

naive_B_cell_Moderate

class_switched_memory_B_cell_Critical

immature_B_cell_Critical

naive_B_cell_Critical

P-value distributions stratified by expression level
For each replicate, calculate average log-normalized counts, using scuttle::calculateAverage().
## Calculate average counts for each replicate
avg_counts <- map_depth(sce_objects, 2,
~ calculateAverage(counts(.x))
)
## Split res_tables per replicate
res_tables_split <- map(res_tables, ~ split(.x, .x$replicate))
## Add average counts to results tables
## Note that for the 'combined' celltypes, the average counts will be the same
## for each celltype contrast
res_tables_split <- map2(
res_tables_split, avg_counts,
~ map2(.x, .y, function(res, avg_cnt) {
res$avg_count <- avg_cnt[res$gene]
res
})
)
Make p-value histograms stratified by the average counts.
pval_hist_strat_plots <- map(res_tables_split,
~ imap(.x, function(y, replicate) {
replicate <- str_remove(replicate, "replicate_")
title <- paste("Replicate:", replicate)
pval_hist_strat(y, n_groups = 6) +
ggtitle(title)
})
)
Session info
Session info
#> [1] "2023-07-21 19:16:19 CEST"
#> ─ Session info ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
#> setting value
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#> os Red Hat Enterprise Linux 8.6 (Ootpa)
#> system x86_64, linux-gnu
#> ui X11
#> language (EN)
#> collate en_US.UTF-8
#> ctype en_US.UTF-8
#> tz Europe/Paris
#> date 2023-07-21
#> pandoc 2.13 @ /apps/gent/RHEL8/zen2-ib/software/Pandoc/2.13/bin/ (via rmarkdown)
#>
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